Chlamydiae are obligate intracellular Gram negative bacteria which replicate only in cytoplasmic inclusions of eukaryotic cells. They have a unique developmental cycle that is represented by two major forms, the spore-like elementary body (EB) infectious form, which is transmitted from cell to cell, and the non-infectious, metabolically active reticulate body (RB) which replicates within the host-cell.
The genus Chlamydia contains at least five species of obligate parasitic bacteria: Chlamydia psittaci, C. pecorum, C. pneumoniae, C. muridarum, and C. trachomatis. This unique genus causes a variety of diseases in humans, mammals, and birds. Chlamydia trachomatis and C. pneumoniae are important human pathogens. The recently defined species C. pneumoniae (Grayston 1989) is now recognized as a major cause of respiratory tract infections (Grayston 1993) and data are now growing for an association with atherosclerosis. The association is supported by seroepidemiological studies, studies demonstrating the presence of the bacterium in the atherosclerotic lesions, studies showing C. pneumoniae capability to replicate in the different cell types present in the atherosclerotic lesions, interventional trials with antibiotics in patients with coronary artery disease and experimental respiratory tract infection in rabbits or apolipoprotein-E deficient mice which leads to inflammatory changes in the aorta (Danesh 1997, Fong 1997, Laitinen 1997). Overall, those data implicate C. pneumoniae as a causative and/or aggravating factor of atherosclerosis.
C. trachomatis is a major human pathogen that is transmitted from human to human (there is no known animal reservoir). It causes ocular and genital infections that can result in long term sequelae. Trachoma, a Chlamydial ocular infection, is endemic in several developing countries and is the leading cause of preventable blindness worldwide with millions of people affected by the disease. Genital Chlamydial infections constitute the most common bacterial sexually transmitted disease (STD). In 1996, WHO generated a new set of global estimates for four major STDs drawing an extensive review of the published and unpublished prevalence data (Gerbase 1998). It has been estimated that in 1995, 4 and 5.2 million new cases of C. trachomatis infection occurred in individuals aged 15-49 for North America and Western Europe, respectively. Data show higher infection rates in women as compared to men. Higher incidence is also found in adolescent and young adults—approximately 70% of the Chlamydial infections being reported in the 15-24 year age group. There is a clear need for effective vaccines against Chlamydia trachomatis and C. pneumoniae. 
C. psittaci causes psitacosis in humans, and in animals, C. psittaci can cause a diverse range of disease in livestock, poultry, turkeys and companion birds. The known C. psittaci strains have been grouped into eight biovars (Perez-Martinez, J A and J Storz, 1985). Strains of serovar 1 are mainly associated with intestinal infections and abortions, while strains of serovar 2 cause polyarthritis, encephalitis, and conjunctivitis in ruminants. Avian strains of C. psittaci cause respiratory problems and diarrhea in birds (Storz, 1988). The organism can also be transmitted to humans from these animals, and outbreaks have been documented in animal production workers. Thus, there is a need for an effective vaccine against C. psittaci for mammalian and avian species.
A highly conserved plasmid of approximately 7.5 kb, is present in almost all strains of C. trachomatis with copy numbers estimated to range from 4 (Pickett et al., 2005) to 10 (Tam et al., 1992) copies per cell. The role of this plasmid is unknown. However, at least one of the plasmid-encoded ORFs is expressed during infection (Comanducci et al., 1993). Naturally occurring plasmid-deficient clinical isolates are extremely rare; only three strains have been described (Peterson et al., 1990; Farencena et al., 1997; Stothard et al., 1998). In contrast, Matsumoto et al. described the isolation and characterization of three plasmid-deficient C. trachomatis strains that occur naturally in tissue-culture propagated cultures at an estimated rate of 1% (Matsumoto et al., 1998). The derivatives identified by Matsumoto et al. appeared unable to accumulate glycogen within the intracytoplasmic inclusions that are formed by the bacteria as they grow. No other phenotypic changes were detected that could be attributed to the presence of the plasmid (Miyashita et al., 2000).
Currently, a genetic system for use in Chlamydiae is lacking. A better understanding of the mechanisms by which the conserved plasmid, a potential gene delivery vector, is maintained, and the ability to generate at high efficiency plasmid-deficient derivatives of the most highly characterized Chlamydiae for use as recipient strains would advance progress in this area.